Geo Pertea

Abstract Divergent transcription from bidirectional promoters is frequently observed in eukaryotic genomes, but the biological relevance of divergent RNA transcripts (DT) is unknown. We identified and characterized BDNF-DT, a novel DT gene, and BDNF-AS-DT, a novel readthrough gene, in the locus containing BDNF, a gene with key roles in neuronal development, differentiation, and synaptic plasticity.

Abstract Accurate assembly of rRNA-depleted (total) RNA sequencing (RNA-seq) remains challenging because existing methods often conflate incomplete, nascent RNA with fully processed mature isoforms, leading to misassemblies and quantification errors. Here, we present StringTie3, a major update to the widely used StringTie assembler, specifically designed for total RNA-seq.

Abstract Accurate assembly of rRNA-depleted (total) RNA-seq remains challenging because existing methods often conflate incomplete, nascent RNA with fully processed mature isoforms, leading to misassemblies and quantification errors that skew downstream analyses. Here, we present StringTie3, a major update to the widely used StringTie assembler, specifically designed for total RNA-seq.